Empirical trees parameter estimation based on simulated trees

“SBFUSED_input.RData” is the main input data that was generated from simulations using the central high-performance computer cluster of ETH Zurich (Brutus) and the R-package TreeSimGM (Hagen, O., Stadler, T. 2013). Inputs from “treebase_output.RData” (that can be found at “data-set_empirical_trees.zip”) are also used, once we use here empirical trees for the fitting. For more details please consult the respective R-package tutorials. All other files are the sub products of the “procedure_rscript.R” script. More details can be found at the methodology section. Figure 3 originates mainly from “SBep_output.RData”, “SBleast.square_output.RData” and “plot_script.R”. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material."SBFUSED_input.RData"为本研究的核心输入数据集，其生成依托苏黎世联邦理工学院（ETH Zurich）高性能计算集群Brutus，以及R语言扩展包TreeSimGM（Hagen, O., Stadler, T. 2013）。当采用经验树开展模型拟合时，本研究同时使用了来自"treebase_output.RData"的输入数据，该数据集可在压缩包"data-set_empirical_trees.zip"中获取。如需了解更多细节，请查阅对应R包的官方教程。所有其余文件均为"procedure_rscript.R"脚本的衍生产物，相关详细说明可参见研究的方法学章节。图3的可视化数据主要源自"SBep_output.RData"、"SBleast.square_output.RData"以及"plot_script.R"。 需特别说明的是，本数据集并未涵盖研究中使用的全部R脚本——尤其是涉及模型行为绘图与分析的相关脚本。由于本研究依托集群计算机开展了大量模拟实验，生成了随迭代更新的多组输出文件、代码脚本与CSV格式参数表，因此完整的脚本集合并未包含在此数据集中。若您计划开展类似实验，我们强烈建议您先研读TreeSimGM R包的官方帮助文档。